title: Tracking the establishment of local endemic populations of an emergent enteric pathogen.
abstract: Shigella sonnei is a human-adapted pathogen that is emerging globally as the dominant agent of bacterial dysentery. To investigate local establishment, we sequenced the genomes of 263 Vietnamese S. sonnei isolated over 15 y. Our data show that S. sonnei was introduced into Vietnam in the 1980s and has undergone localized clonal expansion, punctuated by genomic fixation events through periodic selective sweeps. We uncover geographical spread, spatially restricted frontier populations, and convergent evolution through local gene pool sampling. This work provides a unique, high-resolution insight into the microevolution of a pioneering human pathogen during its establishment in a new host population.
authors.affiliation: Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia.
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Holt
authors.forename: Tran Vu
authors.initials: TV
authors.lastname: Thieu Nga
authors.forename: Duy Pham
authors.initials: DP
authors.lastname: Thanh
authors.forename: Ha
authors.initials: H
authors.lastname: Vinh
authors.forename: Dong Wook
authors.initials: DW
authors.lastname: Kim
authors.forename: My Phan
authors.initials: MP
authors.lastname: Vu Tra
authors.forename: James I
authors.initials: JI
authors.lastname: Campbell
authors.forename: Nguyen Van Minh
authors.initials: NV
authors.lastname: Hoang
authors.forename: Nguyen Thanh
authors.initials: NT
authors.lastname: Vinh
authors.forename: Pham Van
authors.initials: PV
authors.lastname: Minh
authors.forename: Cao Thu
authors.initials: CT
authors.lastname: Thuy
authors.forename: Tran Thi Thu
authors.initials: TT
authors.lastname: Nga
authors.forename: Corinne
authors.initials: C
authors.lastname: Thompson
authors.forename: Tran Thi Ngoc
authors.initials: TT
authors.lastname: Dung
authors.forename: Nguyen Thi Khanh
authors.initials: NT
authors.lastname: Nhu
authors.forename: Phat Voong
authors.initials: PV
authors.lastname: Vinh
authors.forename: Pham Thi Ngoc
authors.initials: PT
authors.lastname: Tuyet
authors.forename: Hoang Le
authors.initials: HL
authors.lastname: Phuc
authors.forename: Nguyen Thi Nam
authors.initials: NT
authors.lastname: Lien
authors.forename: Bui Duc
authors.initials: BD
authors.lastname: Phu
authors.forename: Nguyen Thi Thuy
authors.initials: NT
authors.lastname: Ai
authors.forename: Nguyen Manh
authors.initials: NM
authors.lastname: Tien
authors.forename: Nguyen
authors.initials: N
authors.lastname: Dong
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Parry
authors.forename: Tran Tinh
authors.initials: TT
authors.lastname: Hien
authors.forename: Jeremy J
authors.initials: JJ
authors.lastname: Farrar
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
authors.forename: Stephen
authors.initials: S
authors.lastname: Baker
mesh_terms: D000900:Anti-Bacterial Agents / Q000627:therapeutic use; D002648:Child; D002675:Child, Preschool; D002876:Chromosomes, Bacterial / Q000235:genetics; D002939:Ciprofloxacin / Q000627:therapeutic use; D004405:Dysentery, Bacillary / Q000188:drug therapy / Q000453:epidemiology* / Q000382:microbiology; D019353:Endemic Diseases; D019143:Evolution, Molecular; D024841:Fluoroquinolones / Q000627:therapeutic use; D000077734:Gatifloxacin; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods; D005843:Geography; D006801:Humans; D007223:Infant; D008969:Molecular Sequence Data; D059645:Mutation Rate; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012764:Shigella sonnei / Q000145:classification / Q000235:genetics* / Q000502:physiology; D014744:Vietnam / Q000453:epidemiology
chemical_list: D000900:Anti-Bacterial Agents; D024841:Fluoroquinolones; D002939:Ciprofloxacin; D000077734:Gatifloxacin
keywords: drug resistance; enteric disease; genomics; phylogeography